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Home > Departments > Microbiology > Jacques OBERTO : Cell Biology of Archaea

Jacques OBERTO : Group Presentation

Research conducted by the CBA group is deeply rooted in the biology of Archaea, which are microorganisms discovered in 1977 by Carl Woese. In the tree of life, the Archaea constitute a new domain in its own right, next to the Eukarya domain and the Bacteria domain. A key feature of these Archaea consists of their particular natural environments which often includes one or more condition(s): temperature, pH, salinity, anaerobic and barometric pressure. Archaea therefore extend life in environments where no other organism is capable of surviving. To better understand the evolutionary mechanisms that led to the existence of Archaea, we use a multidisciplinary approach involving genetics, genomics, bioinformatics and biochemistry. Three main topics are currently being pursued: the evolution and genome dynamics in the Archaea Thermococcales; the characterization of the KEOPS complex and prokaryotic genomes bioinformatics.

Project

1) Evolution and genome dynamics in the Archaea Thermococcales.

We study the evolution of genetic information in Archaea of the order Thermococcales. These anaerobic hyperthermophilic organisms evolve rapidly, which seems to be related to the particular conditions of their habitat consisting of black smokers on the ocean floor. We observe the impact of mobile elements (plasmids and viruses) in this evolution. Several new archeal plasmids and strains containing them have been characterized in the laboratory (1, 2). The discovery of membrane vesicles produced by these organisms could also explain the transfer of genetic information between different Archaea and also between Archaea and Bacteria (3-5). With the establishment of a dedicated platform to cultivate hyperthermophilic anaerobes, we are able to reproduce the ideal conditions for growing these extremophile Archaea in the laboratory (Figure 1).

Anaerobic chamber - Archaea
Anaerobic chamber for the manipulation of Archaea Thermococcales

We develop Thermococcales genetics in the model organism Thermococcus kodakarensis. A new species, Thermococcus nautili was characterized in the laboratory (6) and its genome has been determined (7). We develop, in parallel, in silico bioinformatic analysis of these prokaryotic genomes through the deployment of a suite of dedicated web services (8-11), see also below. The study of the dynamics and the maintenance of this genetic information is also pursued by the characterization of novel DNA topoisomerases in the three domains of life (12-14).

2) Characterization of the KEOPS complex.

The t6A tRNA modification is present in the three domains of life. In Archaea and Eukaryotes, the multi-protein complex KEOPS is responsible for this activity which is carried by bacteria by another complex, DEZ as it was demonstrated in the group Valérie de Crécy-Lagard in United States. This t6A modification is essential: mutations in these complexes are deleterious (15). The proteins making up the archaeal complex KEOPS were overproduced and purified in the laboratory, and their structure was determined in collaboration. We were able to reproduce for the first time the complete t6A modification reaction in vitro using the KEOPS complex purified from the Archaea Pyrococcus abyssi and the yeast Saccharomyces cerevisiae with the addition of protein SUA5 (16). It was also observed that the archaeal KEOPS complex can be replaced in vitro by the bacterial DEZ complex, even if the homology between these complexes is only partial. To better understand the role of the P. abyssi complex KEOPS, the different subunits were purified separately and combined to form a variety of dimers and trimers each tested in t6A reactions, ATP hydrolysis and tRNA binding. This allowed to deduct the role of each subunit and to propose a model for the complete modification reaction (17), see Figure 2. It has also been demonstrated in the laboratory that in vitro synthesis of t6A is possible using yeast SUA5 protein and mitochondrial protein QRI7 (18).

t6A & KEOPS + SUA5
Model for the t6a modification reaction by the KEOPS complex + SUA5 in Eukaryotes and Archaea (Perrochia et al. 2013b).

3) Prokaryotic genomes bioinformatics

For several years, we have been developing software under the form of web services for the handling and analysis of genomic sequences of 3,000 fully sequenced prokaryotic organisms which are maintained locally and updated daily. The BAGET service provides fast and easy access to any gene sequence and to its immediate context from any of these organisms . FITBAR predicts regulons across entire genomes on the basis of specific sites provided by the user . ABSYNTE can analyze the conservation of gene order (synteny) in a user-selected list of genomes . SYNTTAX allows synteny analysis according to the taxonomic classification of the different species.

BAGET: http://archaea.u-psud.fr/bin/baget.dll
FITBAR: http://archaea.u-psud.fr/fitbar
ABSYNTE: http://archaea.u-psud.fr/absynte
SYNTTAX: http://archaea.u-psud.fr/synttax

Genomic web services developed in the group

Keywords

Archaea, Thermococcales, genetics, genomics, genome evolution, bioinformatics, biochemistry, tRNA modification.

Contact


OBERTO Jacques [Senior Researcher - CNRS]
Cell Biology of Archae [Leader]
01 69 82 61 69 Gif - Bât 12

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